Graph Theory Analysis of Brain MRI Data

Documentation for package ‘brainGraph’ version 2.2.0

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-- A --

aal116	Coordinates for data from the AAl116 atlas
aal2.120	Coordinates for data from the AAL2 atlas
aal2.94	Coordinates for data from the AAL2 atlas
aal90	Coordinates for data from the AAl90 atlas
analysis_random_graphs	Perform an analysis with random graphs for brain MRI data
aop	Approaches to estimate individual network contribution
apply_thresholds	Threshold additional set of matrices

-- B --

bg_to_mediate	Convert brainGraph results to "mediate" object
brainGraph_boot	Bootstrapping for global graph measures
brainGraph_GLM	Fit linear models at each vertex of a graph
brainGraph_GLM_design	Create a design matrix for linear model analysis
brainGraph_GLM_fit_f	Fit linear models for t contrasts
brainGraph_GLM_fit_t	Fit linear models for t contrasts
brainGraph_init	Initialize variables for further use in brainGraph
brainGraph_mediate	Mediation analysis with brain graph measures as mediator variables
brainGraph_permute	Permutation test for group difference of graph measures
brainsuite	Coordinates for data from BrainSuite atlas

-- C --

centr_betw_comm	Calculate communicability betweenness centrality
centr_lev	Calculate a vertex's leverage centrality
coeff_var	Calculate coefficient of variation
communicability	Calculate communicability
contract_brainGraph	Contract graph vertices based on brain lobe and hemisphere
cor.diff.test	Calculate the p-value for differences in correlation coefficients
corr.matrix	Calculate correlation matrix and threshold
CountEdges	Count number of edges of a brain graph
count_homologous	Count number of edges of a brain graph
count_interlobar	Count number of edges of a brain graph
craddock200	Coordinates for data from the Craddock200 atlas
create_mats	Create connection matrices for tractography or fMRI data

-- D --

DataTables	Create a data table with graph global and vertex measures
destrieux	Coordinates for data from the Destrieux atlas
destrieux.scgm	Coordinates for data from the Destrieux atlas
dk	Coordinates for data from the Desikan-Killiany atlas
dk.scgm	Coordinates for data from the Desikan-Killiany atlas
dkt	Coordinates for data from the Desikan-Killiany-Tourville atlas
dkt.scgm	Coordinates for data from the Desikan-Killiany-Tourville atlas
dosenbach160	Coordinates for data from the Dosenbach160 atlas

-- E --

edge_asymmetry	Calculate an asymmetry index based on edge counts
edge_spatial_dist	Calculate Euclidean distance of edges and vertices
efficiency	Calculate graph global, local, or nodal efficiency
Extract.brainGraph_resids	Linear model residuals in structural covariance networks

-- G --

gateway_coeff	Gateway coefficient, participation coefficient, and within-mod degree z-score
get.resid	Linear model residuals in structural covariance networks
GLMfit	Fit linear models for t contrasts
GraphDistances	Calculate Euclidean distance of edges and vertices
graph_attr_dt	Create a data table with graph global and vertex measures

-- H --

Coordinates for data from Harvard-Oxford atlas

-- I --

Approaches to estimate individual network contribution

-- L --

loo	Approaches to estimate individual network contribution
lpba40	Coordinates for data from the LONI probabilistic brain atlas

-- M --

make_brainGraph	Create a brainGraph object
make_ego_brainGraph	Create a graph of the union of multiple vertex neighborhoods
make_empty_brainGraph	Create an empty graph with attributes for brainGraph
make_glm_brainGraph	Create a graph with GLM-specific attributes
make_intersection_brainGraph	Create the intersection of graphs based on a logical condition
make_mediate_brainGraph	Create a graph with mediation-specific attributes
make_nbs_brainGraph	Create a graph with NBS-specific attributes
mtpc	Multi-threshold permutation correction

-- N --

NBS	Network-based statistic for brain MRI data

-- P --

part_coeff	Gateway coefficient, participation coefficient, and within-mod degree z-score
plot.bg_GLM	Plot GLM diagnostics for a brain network
plot.brainGraph	Plot a brain graph with a specific spatial layout
plot.brainGraph_boot	Plot bootstrap output of global graph measures across densities
plot.brainGraph_GLM	Plot a graph with results from brainGraph_GLM
plot.brainGraph_mediate	Plot a graph with results from a mediation analysis
plot.brainGraph_mtpc	Plot a graph with results from MTPC
plot.brainGraph_NBS	Plot a graph with results from the network-based statistic
plot.brainGraph_permute	Plot results from permutation testing
plot.brainGraph_resids	Plot model residuals for each brain region
plot.mtpc	Plot statistics from an MTPC analysis
plot_brainGraph	Plot a brain graph with a specific spatial layout
plot_brainGraph_gui	GUI for plotting graphs overlaid on an MNI152 image or in a circle.
plot_brainGraph_list	Write PNG files for a list of graphs
plot_brainGraph_multi	Save PNG of three views of a brain graph
plot_corr_mat	Plot a correlation matrix
plot_global	Plot global graph measures across densities
plot_rich_norm	Plot normalized rich club coefficients against degree threshold
plot_vertex_measures	Plot vertex-level graph measures at a single density or threshold
plot_volumetric	Plot group distributions of volumetric measures for a given brain region

-- R --

RandomGraphs	Simulate N random graphs w/ same clustering and degree sequence as the input.
RichClub	Rich club calculations
rich_club_attrs	Assign graph attributes based on rich-club analysis
rich_club_coeff	Rich club calculations
rich_club_norm	Rich club calculations
rich_core	Rich club calculations
robustness	Analysis of network robustness

-- S --

set_brainGraph_attr	Set graph, vertex, and edge attributes common in MRI analyses
sim.rand.graph.clust	Simulate N random graphs w/ same clustering and degree sequence as the input.
sim.rand.graph.par	Simulate N random graphs w/ same clustering and degree sequence as the input.
small.world	Calculate graph small-worldness
summary.bg_GLM	Print a summary from brainGraph_GLM analysis
summary.bg_mediate	Print a summary from a brainGraph mediation analysis
summary.brainGraph	Print a summary of a brainGraph object
summary.brainGraph_boot	Bootstrapping for global graph measures
summary.brainGraph_permute	Print a summary from a permutation analysis
summary.brainGraph_resids	Linear model residuals in structural covariance networks
summary.mtpc	Multi-threshold permutation correction
summary.NBS	Network-based statistic for brain MRI data
symmetrize_array	Create a symmetric matrix
symmetrize_mats	Create a symmetric matrix
s_core	Calculate the s-core of a network

-- V --

VertexRoles	Gateway coefficient, participation coefficient, and within-mod degree z-score
vertex_attr_dt	Create a data table with graph global and vertex measures
vertex_spatial_dist	Calculate Euclidean distance of edges and vertices
vulnerability	Calculate graph vulnerability

-- W --

within_module_deg_z_score	Gateway coefficient, participation coefficient, and within-mod degree z-score
write_brainnet	Write files to be used for visualization with BrainNet Viewer

-- X --

Transform edge weights

-- misc --

Linear model residuals in structural covariance networks